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- PDB-9wne: Cryo-EM structure of the LbCas12a-Lid2-crRNA-DNA complex -

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Basic information

Entry
Database: PDB / ID: 9wne
TitleCryo-EM structure of the LbCas12a-Lid2-crRNA-DNA complex
Components
  • (DNA (39-MER)) x 2
  • Cpf1
  • crRNA
KeywordsRNA BINDING PROTEIN / CRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


: / CRISPR-associated endonuclease Cpf1 PI domain / : / CRISPR-associated endonuclease Cpf1 REC2 domain / CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Cpf1
Similarity search - Component
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsOmura, S.N. / Warren Villegas, R. / Van der Oost, J. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Engineering and characterization of a novel Cas12a nickase
Authors: Warren Villegas, R. / Omura, S.N. / Castro, D.R. / Sudfeld, C. / Luteijn, M. / Morinaga, H. / Inoue, W.J. / Shuto, Y. / Vleesschauwer, D.D. / Staals, R.H.J. / Nureki, O. / Wu, W.Y. / Van der Oost, J.
History
DepositionSep 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cpf1
B: crRNA
C: DNA (39-MER)
D: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,4528
Polymers182,3554
Non-polymers974
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (39-MER)


Mass: 12137.806 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)
#4: DNA chain DNA (39-MER)


Mass: 11870.622 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Cpf1


Mass: 144912.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DWE3
#2: RNA chain crRNA


Mass: 13433.973 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)

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Non-polymers , 2 types, 23 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1LbCas12a-Lid2.3-crRNA-target DNACOMPLEX#1-#40MULTIPLE SOURCES
2crRNA-target DNACOMPLEX#2-#41SYNTHETIC
3LbCas12a-Lid2.3COMPLEX#11RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Servalcat0.4.131model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100683 / Symmetry type: POINT

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